Starting phenix.real_space_refine on Wed Jul 30 04:01:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p47_20245/07_2025/6p47_20245.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p47_20245/07_2025/6p47_20245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p47_20245/07_2025/6p47_20245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p47_20245/07_2025/6p47_20245.map" model { file = "/net/cci-nas-00/data/ceres_data/6p47_20245/07_2025/6p47_20245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p47_20245/07_2025/6p47_20245.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 7872 2.51 5 N 1928 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11972 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5986 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 693} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: B Time building chain proxies: 11.96, per 1000 atoms: 1.00 Number of scatterers: 11972 At special positions: 0 Unit cell: (83.661, 119.667, 116.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 2090 8.00 N 1928 7.00 C 7872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.01 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.01 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.4 seconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2764 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 59.2% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.503A pdb=" N GLU A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 105 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.991A pdb=" N TYR A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.635A pdb=" N ILE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.814A pdb=" N LEU A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.739A pdb=" N ILE A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 327 removed outlier: 4.014A pdb=" N GLN A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.690A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 376 removed outlier: 4.432A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 376 " --> pdb=" O CYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 401 removed outlier: 3.528A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 446 through 462 removed outlier: 3.730A pdb=" N SER A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 460 " --> pdb=" O CYS A 456 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 486 removed outlier: 4.131A pdb=" N ILE A 467 " --> pdb=" O TRP A 463 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 537 removed outlier: 3.631A pdb=" N MET A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 516 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 572 removed outlier: 3.537A pdb=" N TYR A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 637 removed outlier: 3.756A pdb=" N GLN A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN A 623 " --> pdb=" O TRP A 619 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Proline residue: A 628 - end of helix removed outlier: 3.826A pdb=" N MET A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.564A pdb=" N TYR A 654 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.766A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.506A pdb=" N VAL A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.715A pdb=" N LEU A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 741 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.512A pdb=" N PHE A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.591A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 834 " --> pdb=" O HIS A 830 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 868 Processing helix chain 'A' and resid 868 through 880 removed outlier: 3.701A pdb=" N LEU A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.502A pdb=" N GLU B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 removed outlier: 3.992A pdb=" N TYR B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.635A pdb=" N ILE B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.813A pdb=" N LEU B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.740A pdb=" N ILE B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 327 removed outlier: 4.014A pdb=" N GLN B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP B 327 " --> pdb=" O TYR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.690A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 376 removed outlier: 4.431A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 376 " --> pdb=" O CYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 401 removed outlier: 3.527A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.730A pdb=" N SER B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL B 460 " --> pdb=" O CYS B 456 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 486 removed outlier: 4.131A pdb=" N ILE B 467 " --> pdb=" O TRP B 463 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 480 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 537 removed outlier: 3.632A pdb=" N MET B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 509 " --> pdb=" O PRO B 505 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 516 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 535 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 572 removed outlier: 3.537A pdb=" N TYR B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B 548 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE B 558 " --> pdb=" O LYS B 554 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 637 removed outlier: 3.755A pdb=" N GLN B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN B 623 " --> pdb=" O TRP B 619 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU B 624 " --> pdb=" O ASN B 620 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 627 " --> pdb=" O GLN B 623 " (cutoff:3.500A) Proline residue: B 628 - end of helix removed outlier: 3.826A pdb=" N MET B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 636 " --> pdb=" O ASN B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 655 removed outlier: 3.564A pdb=" N TYR B 654 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.766A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.507A pdb=" N VAL B 694 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 747 removed outlier: 3.715A pdb=" N LEU B 735 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.513A pdb=" N PHE B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 removed outlier: 3.591A pdb=" N TRP B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 834 " --> pdb=" O HIS B 830 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 840 " --> pdb=" O LEU B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 868 Processing helix chain 'B' and resid 868 through 880 removed outlier: 3.701A pdb=" N LEU B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 876 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 877 " --> pdb=" O TYR B 873 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS B 880 " --> pdb=" O GLN B 876 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 removed outlier: 3.786A pdb=" N LEU A 146 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 190 " --> pdb=" O LEU A 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 146 removed outlier: 3.786A pdb=" N LEU B 146 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 190 " --> pdb=" O LEU B 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 524 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3515 1.34 - 1.46: 2910 1.46 - 1.58: 5749 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 12298 Sorted by residual: bond pdb=" C LEU B 627 " pdb=" N PRO B 628 " ideal model delta sigma weight residual 1.336 1.369 -0.034 9.80e-03 1.04e+04 1.17e+01 bond pdb=" C LEU A 627 " pdb=" N PRO A 628 " ideal model delta sigma weight residual 1.336 1.369 -0.033 9.80e-03 1.04e+04 1.12e+01 bond pdb=" N PRO A 421 " pdb=" CD PRO A 421 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.01e+00 bond pdb=" N PRO B 421 " pdb=" CD PRO B 421 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 7.96e+00 bond pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 1.469 1.487 -0.018 7.40e-03 1.83e+04 6.08e+00 ... (remaining 12293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 15572 2.12 - 4.25: 860 4.25 - 6.37: 147 6.37 - 8.49: 61 8.49 - 10.61: 24 Bond angle restraints: 16664 Sorted by residual: angle pdb=" CA PRO A 340 " pdb=" C PRO A 340 " pdb=" N ASP A 341 " ideal model delta sigma weight residual 116.20 109.36 6.84 8.00e-01 1.56e+00 7.31e+01 angle pdb=" CA PRO B 340 " pdb=" C PRO B 340 " pdb=" N ASP B 341 " ideal model delta sigma weight residual 116.20 109.37 6.83 8.00e-01 1.56e+00 7.29e+01 angle pdb=" N LEU B 503 " pdb=" CA LEU B 503 " pdb=" C LEU B 503 " ideal model delta sigma weight residual 111.36 119.69 -8.33 1.09e+00 8.42e-01 5.84e+01 angle pdb=" N LYS A 862 " pdb=" CA LYS A 862 " pdb=" CB LYS A 862 " ideal model delta sigma weight residual 110.90 100.75 10.15 1.33e+00 5.65e-01 5.83e+01 angle pdb=" N LEU A 503 " pdb=" CA LEU A 503 " pdb=" C LEU A 503 " ideal model delta sigma weight residual 111.36 119.68 -8.32 1.09e+00 8.42e-01 5.83e+01 ... (remaining 16659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 6170 17.23 - 34.46: 824 34.46 - 51.69: 156 51.69 - 68.92: 72 68.92 - 86.15: 18 Dihedral angle restraints: 7240 sinusoidal: 2950 harmonic: 4290 Sorted by residual: dihedral pdb=" CB CYS B 349 " pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " pdb=" CB CYS B 807 " ideal model delta sinusoidal sigma weight residual -86.00 -146.80 60.80 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CB CYS A 349 " pdb=" SG CYS A 349 " pdb=" SG CYS A 807 " pdb=" CB CYS A 807 " ideal model delta sinusoidal sigma weight residual -86.00 -146.80 60.80 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CA LEU B 123 " pdb=" C LEU B 123 " pdb=" N VAL B 124 " pdb=" CA VAL B 124 " ideal model delta harmonic sigma weight residual -180.00 -151.43 -28.57 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1457 0.077 - 0.155: 282 0.155 - 0.232: 58 0.232 - 0.310: 9 0.310 - 0.387: 10 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CA THR B 504 " pdb=" N THR B 504 " pdb=" C THR B 504 " pdb=" CB THR B 504 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA THR A 504 " pdb=" N THR A 504 " pdb=" C THR A 504 " pdb=" CB THR A 504 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA ASP B 353 " pdb=" N ASP B 353 " pdb=" C ASP B 353 " pdb=" CB ASP B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 1813 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 420 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO A 421 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 420 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B 421 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 421 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 421 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 340 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.67e+00 pdb=" C PRO B 340 " -0.054 2.00e-02 2.50e+03 pdb=" O PRO B 340 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP B 341 " 0.018 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3054 2.77 - 3.31: 11735 3.31 - 3.84: 20391 3.84 - 4.37: 23821 4.37 - 4.90: 37772 Nonbonded interactions: 96773 Sorted by model distance: nonbonded pdb=" O ILE A 743 " pdb=" OG1 THR A 747 " model vdw 2.243 3.040 nonbonded pdb=" O ILE B 743 " pdb=" OG1 THR B 747 " model vdw 2.244 3.040 nonbonded pdb=" O GLN B 506 " pdb=" OG SER B 510 " model vdw 2.271 3.040 nonbonded pdb=" O GLN A 506 " pdb=" OG SER A 510 " model vdw 2.271 3.040 nonbonded pdb=" O VAL A 476 " pdb=" OG SER A 480 " model vdw 2.280 3.040 ... (remaining 96768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.410 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 12304 Z= 0.347 Angle : 1.211 10.613 16676 Z= 0.705 Chirality : 0.072 0.387 1816 Planarity : 0.009 0.102 2066 Dihedral : 17.018 86.147 4458 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.77 % Favored : 90.66 % Rotamer: Outliers : 3.68 % Allowed : 11.50 % Favored : 84.82 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.94 (0.15), residues: 1414 helix: -4.01 (0.10), residues: 732 sheet: -4.06 (0.44), residues: 54 loop : -3.74 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 397 HIS 0.005 0.001 HIS A 830 PHE 0.021 0.002 PHE B 231 TYR 0.034 0.002 TYR A 306 ARG 0.014 0.001 ARG A 420 Details of bonding type rmsd hydrogen bonds : bond 0.30479 ( 524) hydrogen bonds : angle 10.25683 ( 1566) SS BOND : bond 0.00986 ( 6) SS BOND : angle 2.08683 ( 12) covalent geometry : bond 0.00717 (12298) covalent geometry : angle 1.20984 (16664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 350 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.3007 (tmm) cc_final: 0.2506 (ttp) REVERT: A 403 GLU cc_start: 0.7830 (pt0) cc_final: 0.7386 (pt0) REVERT: A 428 ASN cc_start: 0.8229 (p0) cc_final: 0.7771 (p0) REVERT: A 463 TRP cc_start: 0.6533 (t-100) cc_final: 0.5998 (t-100) REVERT: A 558 PHE cc_start: 0.8407 (t80) cc_final: 0.7963 (t80) REVERT: A 612 ILE cc_start: 0.9048 (mt) cc_final: 0.7725 (mt) REVERT: A 621 ASN cc_start: 0.8224 (m-40) cc_final: 0.8015 (m110) REVERT: A 667 GLU cc_start: 0.7407 (mp0) cc_final: 0.7132 (mp0) REVERT: A 685 PHE cc_start: 0.8305 (t80) cc_final: 0.8094 (t80) REVERT: A 867 LYS cc_start: 0.8332 (mmtm) cc_final: 0.8100 (mmtp) REVERT: A 870 ARG cc_start: 0.7280 (ttt180) cc_final: 0.7039 (mpt180) REVERT: B 386 MET cc_start: 0.8021 (mmp) cc_final: 0.7818 (mmt) REVERT: B 463 TRP cc_start: 0.7271 (t-100) cc_final: 0.6877 (t-100) REVERT: B 467 ILE cc_start: 0.8558 (mp) cc_final: 0.8279 (mp) REVERT: B 558 PHE cc_start: 0.8037 (t80) cc_final: 0.7632 (t80) REVERT: B 616 LYS cc_start: 0.9221 (tptt) cc_final: 0.8705 (tptp) REVERT: B 685 PHE cc_start: 0.8448 (t80) cc_final: 0.8187 (t80) REVERT: B 867 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8484 (mmmm) outliers start: 48 outliers final: 14 residues processed: 384 average time/residue: 0.2595 time to fit residues: 140.2625 Evaluate side-chains 276 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 865 LYS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 865 LYS Chi-restraints excluded: chain B residue 875 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 143 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 740 ASN B 56 ASN B 143 HIS B 234 ASN B 249 HIS B 621 ASN B 740 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.104930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.088066 restraints weight = 38266.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089285 restraints weight = 27222.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089677 restraints weight = 20442.726| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12304 Z= 0.177 Angle : 0.796 9.037 16676 Z= 0.428 Chirality : 0.046 0.180 1816 Planarity : 0.007 0.061 2066 Dihedral : 7.906 83.417 1620 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.98 % Favored : 90.74 % Rotamer: Outliers : 2.61 % Allowed : 19.63 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.18), residues: 1414 helix: -2.17 (0.15), residues: 800 sheet: -3.71 (0.54), residues: 44 loop : -3.72 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 397 HIS 0.003 0.001 HIS A 275 PHE 0.022 0.002 PHE A 385 TYR 0.019 0.002 TYR B 242 ARG 0.007 0.001 ARG A 70 Details of bonding type rmsd hydrogen bonds : bond 0.06637 ( 524) hydrogen bonds : angle 5.91631 ( 1566) SS BOND : bond 0.00427 ( 6) SS BOND : angle 1.52044 ( 12) covalent geometry : bond 0.00375 (12298) covalent geometry : angle 0.79542 (16664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 306 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: A 415 GLN cc_start: 0.7651 (mp-120) cc_final: 0.7409 (mp10) REVERT: A 428 ASN cc_start: 0.8213 (p0) cc_final: 0.7801 (p0) REVERT: A 463 TRP cc_start: 0.6589 (t-100) cc_final: 0.6171 (t-100) REVERT: A 542 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7113 (mmm-85) REVERT: A 558 PHE cc_start: 0.8388 (t80) cc_final: 0.8126 (t80) REVERT: A 678 VAL cc_start: 0.9066 (m) cc_final: 0.8687 (p) REVERT: A 685 PHE cc_start: 0.8564 (t80) cc_final: 0.8172 (t80) REVERT: A 697 ILE cc_start: 0.9391 (pt) cc_final: 0.9067 (mt) REVERT: A 773 MET cc_start: 0.8434 (mtm) cc_final: 0.8184 (mpp) REVERT: A 867 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7524 (mmmt) REVERT: A 870 ARG cc_start: 0.7079 (ttt180) cc_final: 0.6826 (tmt170) REVERT: B 123 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6726 (mm) REVERT: B 294 GLU cc_start: 0.8176 (tp30) cc_final: 0.7814 (tp30) REVERT: B 396 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: B 420 ARG cc_start: 0.7375 (mtt90) cc_final: 0.7028 (mmt90) REVERT: B 463 TRP cc_start: 0.7349 (t-100) cc_final: 0.6865 (t-100) REVERT: B 467 ILE cc_start: 0.8692 (mp) cc_final: 0.8272 (mp) REVERT: B 509 THR cc_start: 0.7749 (m) cc_final: 0.7439 (m) REVERT: B 556 PHE cc_start: 0.8499 (t80) cc_final: 0.8248 (t80) REVERT: B 558 PHE cc_start: 0.7872 (t80) cc_final: 0.7553 (t80) REVERT: B 612 ILE cc_start: 0.8998 (mt) cc_final: 0.8209 (mt) REVERT: B 685 PHE cc_start: 0.8574 (t80) cc_final: 0.8251 (t80) REVERT: B 687 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8894 (mm) REVERT: B 859 ASP cc_start: 0.7786 (m-30) cc_final: 0.7485 (m-30) REVERT: B 867 LYS cc_start: 0.8498 (mmtm) cc_final: 0.8074 (mmmt) outliers start: 34 outliers final: 20 residues processed: 324 average time/residue: 0.2254 time to fit residues: 104.9291 Evaluate side-chains 276 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 851 PHE Chi-restraints excluded: chain B residue 875 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 655 HIS B 414 GLN B 655 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.103935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.087190 restraints weight = 39249.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088427 restraints weight = 26302.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.088596 restraints weight = 19945.787| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12304 Z= 0.180 Angle : 0.771 9.189 16676 Z= 0.411 Chirality : 0.046 0.169 1816 Planarity : 0.006 0.054 2066 Dihedral : 7.140 85.900 1607 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.83 % Favored : 89.89 % Rotamer: Outliers : 3.37 % Allowed : 21.55 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.19), residues: 1414 helix: -1.47 (0.16), residues: 804 sheet: -3.50 (0.55), residues: 44 loop : -3.63 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 397 HIS 0.003 0.001 HIS A 830 PHE 0.026 0.002 PHE A 681 TYR 0.016 0.001 TYR B 306 ARG 0.008 0.001 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.05793 ( 524) hydrogen bonds : angle 5.47028 ( 1566) SS BOND : bond 0.00470 ( 6) SS BOND : angle 1.50592 ( 12) covalent geometry : bond 0.00389 (12298) covalent geometry : angle 0.76998 (16664) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6027 (mm) REVERT: A 192 MET cc_start: 0.2989 (mpp) cc_final: 0.2704 (ttp) REVERT: A 403 GLU cc_start: 0.8153 (pt0) cc_final: 0.7784 (pt0) REVERT: A 415 GLN cc_start: 0.7617 (mp-120) cc_final: 0.7147 (mp10) REVERT: A 428 ASN cc_start: 0.8180 (p0) cc_final: 0.7880 (p0) REVERT: A 463 TRP cc_start: 0.6709 (t-100) cc_final: 0.6251 (t-100) REVERT: A 503 LEU cc_start: 0.9029 (pt) cc_final: 0.8769 (pp) REVERT: A 558 PHE cc_start: 0.8425 (t80) cc_final: 0.8148 (t80) REVERT: A 678 VAL cc_start: 0.9004 (m) cc_final: 0.8681 (p) REVERT: A 685 PHE cc_start: 0.8595 (t80) cc_final: 0.8326 (t80) REVERT: A 697 ILE cc_start: 0.9385 (pt) cc_final: 0.9076 (mt) REVERT: A 870 ARG cc_start: 0.7178 (ttt180) cc_final: 0.6925 (tmt170) REVERT: B 123 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6662 (mm) REVERT: B 323 TYR cc_start: 0.7794 (t80) cc_final: 0.7249 (t80) REVERT: B 332 THR cc_start: 0.7797 (p) cc_final: 0.7551 (t) REVERT: B 396 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: B 415 GLN cc_start: 0.7969 (mp10) cc_final: 0.7557 (mp10) REVERT: B 463 TRP cc_start: 0.7329 (t-100) cc_final: 0.6864 (t-100) REVERT: B 467 ILE cc_start: 0.8616 (mp) cc_final: 0.8195 (mp) REVERT: B 678 VAL cc_start: 0.9164 (m) cc_final: 0.8844 (p) REVERT: B 685 PHE cc_start: 0.8557 (t80) cc_final: 0.8267 (t80) REVERT: B 773 MET cc_start: 0.8480 (mtp) cc_final: 0.8243 (mtm) REVERT: B 851 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: B 867 LYS cc_start: 0.8374 (mmtm) cc_final: 0.8134 (mmtm) outliers start: 44 outliers final: 22 residues processed: 309 average time/residue: 0.2218 time to fit residues: 100.8809 Evaluate side-chains 274 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 63 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 77 optimal weight: 0.0470 chunk 32 optimal weight: 6.9990 chunk 89 optimal weight: 0.0870 chunk 136 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.103727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.087925 restraints weight = 37514.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089643 restraints weight = 24588.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.089979 restraints weight = 17246.192| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12304 Z= 0.148 Angle : 0.752 8.290 16676 Z= 0.391 Chirality : 0.045 0.188 1816 Planarity : 0.005 0.050 2066 Dihedral : 6.294 38.423 1598 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.76 % Favored : 89.96 % Rotamer: Outliers : 3.30 % Allowed : 22.93 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.20), residues: 1414 helix: -1.07 (0.17), residues: 790 sheet: -2.89 (0.65), residues: 44 loop : -3.47 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 273 HIS 0.003 0.000 HIS A 830 PHE 0.045 0.002 PHE A 485 TYR 0.020 0.001 TYR A 242 ARG 0.009 0.001 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.05217 ( 524) hydrogen bonds : angle 5.23856 ( 1566) SS BOND : bond 0.00345 ( 6) SS BOND : angle 1.19701 ( 12) covalent geometry : bond 0.00321 (12298) covalent geometry : angle 0.75168 (16664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 277 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.6037 (mm) REVERT: A 133 GLU cc_start: 0.8307 (tp30) cc_final: 0.7501 (tp30) REVERT: A 386 MET cc_start: 0.8211 (mmt) cc_final: 0.8002 (mmp) REVERT: A 407 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8594 (mm-30) REVERT: A 415 GLN cc_start: 0.7428 (mp-120) cc_final: 0.7051 (mp10) REVERT: A 428 ASN cc_start: 0.8202 (p0) cc_final: 0.7901 (p0) REVERT: A 463 TRP cc_start: 0.6726 (t-100) cc_final: 0.6405 (t-100) REVERT: A 535 ILE cc_start: 0.9113 (tp) cc_final: 0.8815 (tp) REVERT: A 558 PHE cc_start: 0.8369 (t80) cc_final: 0.8046 (t80) REVERT: A 685 PHE cc_start: 0.8766 (t80) cc_final: 0.8322 (t80) REVERT: A 697 ILE cc_start: 0.9402 (pt) cc_final: 0.9129 (mt) REVERT: A 870 ARG cc_start: 0.7228 (ttt180) cc_final: 0.6964 (tmt170) REVERT: B 123 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6693 (mm) REVERT: B 142 MET cc_start: 0.8632 (mmm) cc_final: 0.7937 (mmm) REVERT: B 294 GLU cc_start: 0.8219 (tp30) cc_final: 0.8008 (tp30) REVERT: B 323 TYR cc_start: 0.7847 (t80) cc_final: 0.7229 (t80) REVERT: B 332 THR cc_start: 0.7810 (p) cc_final: 0.7579 (t) REVERT: B 396 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: B 415 GLN cc_start: 0.8058 (mp10) cc_final: 0.7474 (pm20) REVERT: B 463 TRP cc_start: 0.7200 (t-100) cc_final: 0.6774 (t-100) REVERT: B 616 LYS cc_start: 0.9157 (tptt) cc_final: 0.8901 (tptp) REVERT: B 678 VAL cc_start: 0.9148 (m) cc_final: 0.8883 (p) REVERT: B 685 PHE cc_start: 0.8524 (t80) cc_final: 0.8236 (t80) REVERT: B 773 MET cc_start: 0.8505 (mtp) cc_final: 0.8270 (mtm) REVERT: B 851 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7796 (m-80) outliers start: 43 outliers final: 24 residues processed: 308 average time/residue: 0.2006 time to fit residues: 92.7044 Evaluate side-chains 287 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 chunk 107 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.105124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.087366 restraints weight = 37694.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.089390 restraints weight = 22463.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090713 restraints weight = 15974.280| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12304 Z= 0.144 Angle : 0.747 8.885 16676 Z= 0.387 Chirality : 0.045 0.234 1816 Planarity : 0.005 0.051 2066 Dihedral : 5.930 32.087 1594 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.62 % Favored : 90.10 % Rotamer: Outliers : 3.37 % Allowed : 25.00 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.20), residues: 1414 helix: -0.91 (0.17), residues: 804 sheet: -2.62 (0.67), residues: 44 loop : -3.55 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 273 HIS 0.003 0.000 HIS A 830 PHE 0.027 0.002 PHE A 681 TYR 0.017 0.001 TYR B 756 ARG 0.008 0.001 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04866 ( 524) hydrogen bonds : angle 5.06961 ( 1566) SS BOND : bond 0.00313 ( 6) SS BOND : angle 1.09975 ( 12) covalent geometry : bond 0.00308 (12298) covalent geometry : angle 0.74644 (16664) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8487 (tp30) cc_final: 0.7631 (tp30) REVERT: A 192 MET cc_start: 0.2471 (mmt) cc_final: 0.1623 (ttp) REVERT: A 294 GLU cc_start: 0.8323 (tp30) cc_final: 0.7999 (tp30) REVERT: A 428 ASN cc_start: 0.8270 (p0) cc_final: 0.7943 (p0) REVERT: A 463 TRP cc_start: 0.6965 (t-100) cc_final: 0.6566 (t-100) REVERT: A 535 ILE cc_start: 0.9229 (tp) cc_final: 0.9005 (tp) REVERT: A 553 MET cc_start: 0.8041 (tpt) cc_final: 0.7812 (tpt) REVERT: A 558 PHE cc_start: 0.8289 (t80) cc_final: 0.7952 (t80) REVERT: A 685 PHE cc_start: 0.8865 (t80) cc_final: 0.8308 (t80) REVERT: A 870 ARG cc_start: 0.7133 (ttt180) cc_final: 0.6836 (tmt170) REVERT: B 123 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6654 (mm) REVERT: B 332 THR cc_start: 0.7851 (p) cc_final: 0.7546 (t) REVERT: B 396 PHE cc_start: 0.8668 (t80) cc_final: 0.8081 (m-80) REVERT: B 415 GLN cc_start: 0.8113 (mp10) cc_final: 0.7872 (mp10) REVERT: B 463 TRP cc_start: 0.7373 (t-100) cc_final: 0.6866 (t-100) REVERT: B 616 LYS cc_start: 0.9208 (tptt) cc_final: 0.8973 (tptp) REVERT: B 678 VAL cc_start: 0.9209 (m) cc_final: 0.8980 (p) REVERT: B 685 PHE cc_start: 0.8591 (t80) cc_final: 0.8156 (t80) REVERT: B 714 MET cc_start: 0.8635 (pmm) cc_final: 0.8408 (pmm) REVERT: B 773 MET cc_start: 0.8506 (mtp) cc_final: 0.8119 (mtp) REVERT: B 851 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7780 (m-80) outliers start: 44 outliers final: 27 residues processed: 320 average time/residue: 0.2002 time to fit residues: 97.4067 Evaluate side-chains 294 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 765 TYR Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 844 HIS ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.105465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.088403 restraints weight = 38117.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090292 restraints weight = 22205.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.091599 restraints weight = 15870.799| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12304 Z= 0.145 Angle : 0.758 9.297 16676 Z= 0.389 Chirality : 0.045 0.258 1816 Planarity : 0.005 0.052 2066 Dihedral : 5.800 31.201 1594 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.69 % Favored : 90.03 % Rotamer: Outliers : 3.30 % Allowed : 27.30 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.21), residues: 1414 helix: -0.73 (0.18), residues: 804 sheet: -2.39 (0.70), residues: 44 loop : -3.47 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 273 HIS 0.003 0.000 HIS A 830 PHE 0.044 0.002 PHE B 485 TYR 0.016 0.001 TYR A 756 ARG 0.006 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04823 ( 524) hydrogen bonds : angle 5.05220 ( 1566) SS BOND : bond 0.00262 ( 6) SS BOND : angle 1.00684 ( 12) covalent geometry : bond 0.00320 (12298) covalent geometry : angle 0.75730 (16664) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8416 (tp30) cc_final: 0.7745 (tp30) REVERT: A 294 GLU cc_start: 0.8204 (tp30) cc_final: 0.7972 (tp30) REVERT: A 428 ASN cc_start: 0.8262 (p0) cc_final: 0.7925 (p0) REVERT: A 463 TRP cc_start: 0.7010 (t-100) cc_final: 0.6788 (t-100) REVERT: A 539 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: A 553 MET cc_start: 0.7949 (tpt) cc_final: 0.6984 (tpp) REVERT: A 558 PHE cc_start: 0.8329 (t80) cc_final: 0.7933 (t80) REVERT: A 685 PHE cc_start: 0.8819 (t80) cc_final: 0.8238 (t80) REVERT: A 773 MET cc_start: 0.8663 (mtm) cc_final: 0.8459 (mtm) REVERT: A 870 ARG cc_start: 0.7166 (ttt180) cc_final: 0.6813 (tmt170) REVERT: B 123 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6781 (mm) REVERT: B 294 GLU cc_start: 0.8261 (tp30) cc_final: 0.7983 (tp30) REVERT: B 396 PHE cc_start: 0.8674 (t80) cc_final: 0.8102 (m-80) REVERT: B 415 GLN cc_start: 0.8118 (mp10) cc_final: 0.7787 (mp10) REVERT: B 463 TRP cc_start: 0.7343 (t-100) cc_final: 0.6840 (t-100) REVERT: B 558 PHE cc_start: 0.8385 (t80) cc_final: 0.7701 (t80) REVERT: B 678 VAL cc_start: 0.9246 (m) cc_final: 0.9019 (p) REVERT: B 685 PHE cc_start: 0.8801 (t80) cc_final: 0.8289 (t80) REVERT: B 710 GLN cc_start: 0.6851 (tm-30) cc_final: 0.6508 (tm-30) REVERT: B 851 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7788 (m-80) outliers start: 43 outliers final: 27 residues processed: 316 average time/residue: 0.2025 time to fit residues: 95.6327 Evaluate side-chains 295 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 765 TYR Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 HIS B 275 HIS B 418 GLN B 674 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.105693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.088682 restraints weight = 37894.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.090553 restraints weight = 22951.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.091735 restraints weight = 16549.549| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12304 Z= 0.147 Angle : 0.788 10.474 16676 Z= 0.401 Chirality : 0.046 0.241 1816 Planarity : 0.005 0.052 2066 Dihedral : 5.757 31.636 1594 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.55 % Favored : 90.17 % Rotamer: Outliers : 3.76 % Allowed : 28.45 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.21), residues: 1414 helix: -0.65 (0.18), residues: 806 sheet: -2.22 (0.74), residues: 44 loop : -3.44 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 273 HIS 0.003 0.000 HIS A 830 PHE 0.024 0.001 PHE A 485 TYR 0.021 0.001 TYR A 756 ARG 0.007 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 524) hydrogen bonds : angle 5.11626 ( 1566) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.99280 ( 12) covalent geometry : bond 0.00327 (12298) covalent geometry : angle 0.78792 (16664) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 278 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5855 (mm) REVERT: A 133 GLU cc_start: 0.8293 (tp30) cc_final: 0.7654 (tp30) REVERT: A 348 MET cc_start: 0.8010 (ptp) cc_final: 0.7524 (ptt) REVERT: A 403 GLU cc_start: 0.7923 (pt0) cc_final: 0.7658 (pt0) REVERT: A 428 ASN cc_start: 0.8180 (p0) cc_final: 0.7834 (p0) REVERT: A 463 TRP cc_start: 0.7141 (t-100) cc_final: 0.6752 (t-100) REVERT: A 539 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: A 553 MET cc_start: 0.8006 (tpt) cc_final: 0.7059 (tpp) REVERT: A 555 MET cc_start: 0.8798 (tpp) cc_final: 0.8510 (tpp) REVERT: A 558 PHE cc_start: 0.8285 (t80) cc_final: 0.7941 (t80) REVERT: A 685 PHE cc_start: 0.8772 (t80) cc_final: 0.8212 (t80) REVERT: A 773 MET cc_start: 0.8588 (mtm) cc_final: 0.8345 (mtm) REVERT: A 851 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: A 870 ARG cc_start: 0.7154 (ttt180) cc_final: 0.6810 (tmt170) REVERT: B 123 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6875 (mm) REVERT: B 348 MET cc_start: 0.8341 (ptt) cc_final: 0.6826 (ptt) REVERT: B 396 PHE cc_start: 0.8617 (t80) cc_final: 0.8078 (m-80) REVERT: B 415 GLN cc_start: 0.8186 (mp10) cc_final: 0.7982 (mp10) REVERT: B 463 TRP cc_start: 0.7277 (t-100) cc_final: 0.6802 (t-100) REVERT: B 558 PHE cc_start: 0.8374 (t80) cc_final: 0.7719 (t80) REVERT: B 678 VAL cc_start: 0.9206 (m) cc_final: 0.8986 (p) REVERT: B 685 PHE cc_start: 0.8736 (t80) cc_final: 0.8287 (t80) REVERT: B 697 ILE cc_start: 0.9375 (pt) cc_final: 0.9114 (mm) REVERT: B 851 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7780 (m-80) outliers start: 49 outliers final: 29 residues processed: 307 average time/residue: 0.2288 time to fit residues: 107.7767 Evaluate side-chains 296 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 0.1980 chunk 84 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 HIS B 275 HIS B 674 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.106977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.091228 restraints weight = 36895.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.093004 restraints weight = 22742.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.094034 restraints weight = 16500.378| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12304 Z= 0.146 Angle : 0.801 11.386 16676 Z= 0.406 Chirality : 0.046 0.241 1816 Planarity : 0.005 0.051 2066 Dihedral : 5.689 32.381 1594 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.55 % Favored : 90.17 % Rotamer: Outliers : 3.30 % Allowed : 28.76 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.21), residues: 1414 helix: -0.55 (0.18), residues: 806 sheet: -2.10 (0.76), residues: 44 loop : -3.43 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 359 HIS 0.003 0.000 HIS A 830 PHE 0.053 0.001 PHE B 485 TYR 0.014 0.001 TYR A 756 ARG 0.012 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 524) hydrogen bonds : angle 5.10778 ( 1566) SS BOND : bond 0.00254 ( 6) SS BOND : angle 0.94608 ( 12) covalent geometry : bond 0.00327 (12298) covalent geometry : angle 0.80066 (16664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 277 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7883 (tp30) cc_final: 0.7412 (tp30) REVERT: A 348 MET cc_start: 0.7690 (ptp) cc_final: 0.7395 (ptt) REVERT: A 403 GLU cc_start: 0.7732 (pt0) cc_final: 0.7500 (pt0) REVERT: A 428 ASN cc_start: 0.8045 (p0) cc_final: 0.7727 (p0) REVERT: A 463 TRP cc_start: 0.6847 (t-100) cc_final: 0.6352 (t-100) REVERT: A 539 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: A 553 MET cc_start: 0.7945 (tpt) cc_final: 0.7041 (tpp) REVERT: A 558 PHE cc_start: 0.8339 (t80) cc_final: 0.8124 (t80) REVERT: A 685 PHE cc_start: 0.8616 (t80) cc_final: 0.8210 (t80) REVERT: A 773 MET cc_start: 0.8462 (mtm) cc_final: 0.8218 (mtm) REVERT: A 851 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: A 870 ARG cc_start: 0.7191 (ttt180) cc_final: 0.6873 (tmt170) REVERT: B 133 GLU cc_start: 0.7866 (tp30) cc_final: 0.7345 (tp30) REVERT: B 235 ARG cc_start: 0.7906 (mmm160) cc_final: 0.7044 (ttm-80) REVERT: B 268 LEU cc_start: 0.9331 (mt) cc_final: 0.8867 (mt) REVERT: B 396 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: B 415 GLN cc_start: 0.7984 (mp10) cc_final: 0.7665 (mp10) REVERT: B 463 TRP cc_start: 0.6996 (t-100) cc_final: 0.6628 (t-100) REVERT: B 558 PHE cc_start: 0.8345 (t80) cc_final: 0.7784 (t80) REVERT: B 678 VAL cc_start: 0.9185 (m) cc_final: 0.8953 (p) REVERT: B 685 PHE cc_start: 0.8590 (t80) cc_final: 0.8322 (t80) REVERT: B 687 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8851 (mm) REVERT: B 697 ILE cc_start: 0.9272 (pt) cc_final: 0.8963 (mm) REVERT: B 750 MET cc_start: 0.8019 (ppp) cc_final: 0.7791 (ptm) REVERT: B 851 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7823 (m-80) outliers start: 43 outliers final: 27 residues processed: 303 average time/residue: 0.1923 time to fit residues: 89.0852 Evaluate side-chains 294 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 131 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 138 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 HIS B 275 HIS B 330 ASN B 674 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.107556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.091676 restraints weight = 36692.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.093453 restraints weight = 22914.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.094517 restraints weight = 16713.666| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12304 Z= 0.148 Angle : 0.814 11.704 16676 Z= 0.411 Chirality : 0.046 0.271 1816 Planarity : 0.005 0.051 2066 Dihedral : 5.667 33.376 1594 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.97 % Favored : 89.75 % Rotamer: Outliers : 3.07 % Allowed : 29.45 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.21), residues: 1414 helix: -0.50 (0.18), residues: 816 sheet: -1.91 (0.78), residues: 44 loop : -3.49 (0.23), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 359 HIS 0.004 0.001 HIS A 143 PHE 0.052 0.001 PHE B 485 TYR 0.014 0.001 TYR B 756 ARG 0.006 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 524) hydrogen bonds : angle 5.09231 ( 1566) SS BOND : bond 0.00232 ( 6) SS BOND : angle 0.90775 ( 12) covalent geometry : bond 0.00331 (12298) covalent geometry : angle 0.81432 (16664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 283 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7842 (tp30) cc_final: 0.7198 (tp30) REVERT: A 348 MET cc_start: 0.7723 (ptp) cc_final: 0.7433 (ptt) REVERT: A 415 GLN cc_start: 0.6622 (OUTLIER) cc_final: 0.5889 (pm20) REVERT: A 428 ASN cc_start: 0.8068 (p0) cc_final: 0.7744 (p0) REVERT: A 463 TRP cc_start: 0.6845 (t-100) cc_final: 0.6359 (t-100) REVERT: A 553 MET cc_start: 0.7925 (tpt) cc_final: 0.7001 (tpp) REVERT: A 555 MET cc_start: 0.8642 (tpp) cc_final: 0.8427 (tpp) REVERT: A 558 PHE cc_start: 0.8369 (t80) cc_final: 0.8114 (t80) REVERT: A 685 PHE cc_start: 0.8622 (t80) cc_final: 0.8199 (t80) REVERT: A 870 ARG cc_start: 0.7174 (ttt180) cc_final: 0.6863 (tmt170) REVERT: B 133 GLU cc_start: 0.7848 (tp30) cc_final: 0.7312 (tp30) REVERT: B 235 ARG cc_start: 0.7888 (mmm160) cc_final: 0.7016 (ttm-80) REVERT: B 396 PHE cc_start: 0.8530 (t80) cc_final: 0.7999 (m-80) REVERT: B 415 GLN cc_start: 0.7924 (mp10) cc_final: 0.7550 (mp10) REVERT: B 463 TRP cc_start: 0.6955 (t-100) cc_final: 0.6568 (t-100) REVERT: B 558 PHE cc_start: 0.8362 (t80) cc_final: 0.7856 (t80) REVERT: B 685 PHE cc_start: 0.8538 (t80) cc_final: 0.8337 (t80) REVERT: B 687 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8838 (mm) REVERT: B 697 ILE cc_start: 0.9300 (pt) cc_final: 0.8981 (mm) REVERT: B 750 MET cc_start: 0.8077 (ppp) cc_final: 0.7677 (ppp) REVERT: B 851 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7824 (m-80) outliers start: 40 outliers final: 29 residues processed: 306 average time/residue: 0.1990 time to fit residues: 91.8639 Evaluate side-chains 294 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 674 GLN Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 108 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 HIS B 330 ASN B 674 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.105363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089668 restraints weight = 37083.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.091302 restraints weight = 24088.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092367 restraints weight = 17901.512| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12304 Z= 0.187 Angle : 0.858 11.969 16676 Z= 0.438 Chirality : 0.050 0.431 1816 Planarity : 0.005 0.050 2066 Dihedral : 5.724 36.304 1594 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.97 % Favored : 89.75 % Rotamer: Outliers : 2.61 % Allowed : 30.21 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.21), residues: 1414 helix: -0.50 (0.18), residues: 824 sheet: -2.02 (0.77), residues: 44 loop : -3.44 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.003 0.001 HIS A 830 PHE 0.051 0.002 PHE B 485 TYR 0.014 0.001 TYR A 776 ARG 0.006 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04813 ( 524) hydrogen bonds : angle 5.14106 ( 1566) SS BOND : bond 0.00305 ( 6) SS BOND : angle 0.97187 ( 12) covalent geometry : bond 0.00422 (12298) covalent geometry : angle 0.85814 (16664) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8128 (tp30) cc_final: 0.7501 (tp30) REVERT: A 348 MET cc_start: 0.7887 (ptp) cc_final: 0.7551 (ptt) REVERT: A 403 GLU cc_start: 0.7878 (pt0) cc_final: 0.7651 (pt0) REVERT: A 415 GLN cc_start: 0.6778 (mp10) cc_final: 0.5952 (pm20) REVERT: A 428 ASN cc_start: 0.8129 (p0) cc_final: 0.7766 (p0) REVERT: A 463 TRP cc_start: 0.7091 (t-100) cc_final: 0.6540 (t-100) REVERT: A 553 MET cc_start: 0.7992 (tpt) cc_final: 0.7025 (tpp) REVERT: A 558 PHE cc_start: 0.8444 (t80) cc_final: 0.8173 (t80) REVERT: A 685 PHE cc_start: 0.8745 (t80) cc_final: 0.8174 (t80) REVERT: A 851 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8102 (m-80) REVERT: A 870 ARG cc_start: 0.7197 (ttt180) cc_final: 0.6840 (tmt170) REVERT: B 133 GLU cc_start: 0.8151 (tp30) cc_final: 0.7548 (tp30) REVERT: B 235 ARG cc_start: 0.7985 (mmm160) cc_final: 0.7107 (ttm-80) REVERT: B 396 PHE cc_start: 0.8666 (t80) cc_final: 0.8159 (m-80) REVERT: B 415 GLN cc_start: 0.8174 (mp10) cc_final: 0.7578 (pm20) REVERT: B 463 TRP cc_start: 0.7168 (t-100) cc_final: 0.6604 (t-100) REVERT: B 558 PHE cc_start: 0.8436 (t80) cc_final: 0.7693 (t80) REVERT: B 685 PHE cc_start: 0.8699 (t80) cc_final: 0.8457 (t80) REVERT: B 687 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8923 (mm) REVERT: B 697 ILE cc_start: 0.9424 (pt) cc_final: 0.9145 (mm) REVERT: B 851 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7824 (m-80) outliers start: 34 outliers final: 23 residues processed: 290 average time/residue: 0.2088 time to fit residues: 90.8979 Evaluate side-chains 282 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 674 GLN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 HIS B 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.106386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090413 restraints weight = 36728.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092173 restraints weight = 23189.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.093243 restraints weight = 17023.029| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12304 Z= 0.157 Angle : 0.869 11.930 16676 Z= 0.434 Chirality : 0.049 0.373 1816 Planarity : 0.005 0.050 2066 Dihedral : 5.742 36.134 1594 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.69 % Favored : 90.03 % Rotamer: Outliers : 2.45 % Allowed : 30.52 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.21), residues: 1414 helix: -0.45 (0.18), residues: 824 sheet: -1.85 (0.79), residues: 44 loop : -3.40 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 397 HIS 0.003 0.001 HIS A 830 PHE 0.051 0.002 PHE B 485 TYR 0.013 0.001 TYR A 270 ARG 0.009 0.001 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.04694 ( 524) hydrogen bonds : angle 5.13913 ( 1566) SS BOND : bond 0.00247 ( 6) SS BOND : angle 0.93832 ( 12) covalent geometry : bond 0.00356 (12298) covalent geometry : angle 0.86945 (16664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3702.08 seconds wall clock time: 65 minutes 15.49 seconds (3915.49 seconds total)